Dear Amber Users,
I am trying to construct a dipeptide using gamma-amino acid. I have obtained the
parameters using the red server and I use the following script to generate the
prm top and crd files:
GVA=loadmol2 GVA.mol2
loadamberparams GVA.frcmod
gva=sequence { GVA GVA }
solvatebox gva TIP3PBOX 9.00 0.75
saveamberparm gva gva.prmtop gva.prmcrd
quit
When I use the same script for VAL, it works but with GVA, it gives TER
separated units of GVA.
For parameter generation in case of GVA, I have considered the amino acid to be
in the NH-XXXX-CO state. I am a little confused how to go about this and would
very much appreciate any help in this regard.
Best Regards,
Moitrayee
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Received on Thu Feb 21 2013 - 13:30:12 PST
